[Keep in mind I am no longer the lead developer on Minecraft, Jens is. This post is about what I thought about back when I was making it]
If it wasn't for the fact that the default Minecraft character is referred to as “Minecraft Guy” and that I once jokingly answered “Steve?” when asked what his* name was, Minecraft would be a game where gender isn't a gameplay element.
The human model is intended to represent a Human Being. Not a male Human Being or a female Human Being, but simply a Human Being. The blocky shape gives it a bit of a traditional masculine look, but adding a separate female mesh would just make it worse by having one specific model for female Human Beings and male ones. That would force players to make a decisions about gender in a game where gender doesn't even exist.
All the other mobs in the game are genderless and usually exhibit the most prominent traits of both genders. Cows have horns and udders (even if I've later learned that there are some cows where the females do have horns), and the chicken/duck/whatevers have heads that look like roosters, but still lay eggs. For breeding, any animal can breed with any other animal of the same species.
Obviously, I'm not saying this is a good way to deal with gender in all games, as the better your graphics are, and because of how quickly the human mind tries to identify the gender of other humans, you are going to have to make a decision as a developer about gender, but I felt we could get away with it in Minecraft.
There's no point to this post. I just wanted to clarify, so there's an official word on it.
Also, as a fun side fact, it means every character and animal in Minecraft is homosexual because there's only one gender to choose from. Take THAT, homophobes!
* I do regret using masculine terms to talk about the default character. These days I try to use the up-and-coming use of “they” as a genderless pronoun.